Next Generation Sequencing (NGS) is an emerging field applied various biological field. What could be the possibilities of NGS for diagnosing viruses from the clinical samples efficiently and accurately. What are all the merits and demerits are there?
Using RNA-Seq data you can do the following pipeline: [1] de novo assembly the reads into contigs; [2] use Kallisto to calculate the relative abundance of each transcript. [3] use Diamond or BLAST to identify the taxonomy of the best hit for each assembled transcript. [4] filter those transcripts that matches viral sequences. Finally, [5] combines the quantification results and the selected transcripts and rank the virus by abundance.
Hi Dr Mathavan,
I am attaching a copy of our review article exactly focused on your question. Hope you find it useful.
Best wishes,
SD
The data generated by NGS can be analysed in two different ways (a) de novo assembly and (b) reference based assembly. If you know the virus in the clinical sample then reference based assembly is the best approach. In case if you don't know which virus is present in the sample then de novo assembly is the best and the assembled sequence can be blasted against the viral database. Do remember that more than 95% of the reads is of the host. The reads of virus that you are looking for may be less than 1% of the total read. Hope this helps.
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